Your Food’s Bacteria is a Big Data Gold Mine

IBM’s data scientists are pioneering a robust new way to prevent the kind of food contamination that kills thousands of Americans every year (and may well end up killing Chipotle).

The goal—at once futuristic and a little icky—is to track food across the sprawling, global supply chain by sequencing the DNA of the microorganisms that live on it.

Just like our bodies, our food has thousands of these tiny hitchhikers, the vast majority harmless, making up what’s known as a “microbiome.” According to lead researcher Jeff Welser, conditions as diverse as soil and processing methods all influence a food’s microbiome, making the collective DNA of its microorganisms a detailed and unique record of its path to your plate.

The data has huge potential to improve not just food safety, but nutrition and production efficiency. IBM ibm is currently testing the idea in collaboration with food company Mars by tracking the ingredients arriving at one of the company’s dog food plants.

To explain how microbiome testing could improve on current food safety standards, Welser points to the appearance of melamine in Chinese food products in 2008. The problem initially went undetected because, he says, no one was specifically testing for melamine. But a microbiome-based test could detect any shift away from a ‘normal’ baseline, because anything from tampered ingredients to unsafe handling would change a food’s microorganism profile.

Welser points out that most current food safety tests come back negative—which is great, but doesn’t provide a lot of bang for the testing buck. Microbiome testing wouldn’t just improve existing standards, it would also produce a data set with many other applications—something like a Google Analytics for food production.

“Wouldn’t it be great,” he asks, “If every test I did taught me something?”

Microbiome DNA testing could help producers track which healthy microbiomes help meats, fruits, and vegetables stay fresh longer on store shelves. That data could then be used to tailor farming or processing globally to promote microbiomes with preservative properties.

“The other thing you get for free on this,” Welser continues, “Is a really easy and clear way to stop food fraud.” For instance, testing fish would confirm that it’s the species a supplier claims it to be.

Of course, there is something counterintuitive to the idea of making food safer by cataloging the thousands of bacteria living on it. But the public is getting used to the idea that not all microorganisms are bad—probiotic foods, for example, are now widely marketed to consumers hoping to encourage their own bodies’ “good” bacteria.

For more on food safety, watch our video.

For now, selling the public and regulators on microbiome testing is still on the horizon. Welser says broad application will require building a massive database of microbiome profiles. Some databases exist, and IBM is also building its own, while seeking more partners in the food production world to join the project.

“What we’re building up,” says Welser, “Is a database of, here are the bacteria that live in particular kinds of food. Harmful variations, don’t care variations, [or some] that have some benefits for you.”

Raw pet food sales are booming, but are the products safe?

Along with serving grain-free, organic and all natural foods to their cats and dogs, more Americans are dishing out raw food to their pets. In the past year, retail sales of raw freeze-dried dog and cat food jumped 64%, from $25 million to $40 million, and sales of raw frozen pet food jumped 32% from $52 million to $69 million, according to GfK, a market research firm.

Petfood Industry, a trade publication, called the trend part of the “humanization” of pet food, where owners want to provide better nutrition, higher quality and organic ingredients. And now as a corollary to our Paleo diet, they’re embracing raw food as a way of simulating how dogs and cats would eat in the wild.

Proponents of raw pet food, which can be purchased fresh, frozen or freeze dried, claim that it will keep pets healthier, give them shinier coats, healthier skin, and more energy, and keep them free of such problems as obesity and a list of canine and feline diseases. A Survey by Allprovide, a raw pet food company, found that 33 percent of “health conscious” pet owners surveyed said they would be interested in feeding their pets a fresh, raw food diet.

Yet, the trend to go raw is not without controversy — and health concerns. There’s been an uptick in the number of Food and Drug Administration (FDA) recalls of raw pet food because of contamination with listeria, salmonella and E. coli. In July alone, there were four recalls of raw pet food. Vital Essentials’ batches of frozen beef tripe and Stella & Chewy’s batches of chicken freeze-dried dinner patties were among the products recalled, due to potential listeria contamination. Nature’s Variety voluntarily recalled its Instinct Raw Chicken Formula for dogs due to a possible salmonella risk.

However, recalls of pet food of all kinds have become the norm. “In recent years, the whole pet food industry has been heavily scrutinized by the FDA, and it’s part of this drive to move them to the same standards as human food,” says James Marsden, PhD, professor of food safety and security at Kansas State University. The vast majority of recalls have been precautionary, resulting from routine sampling, not pets or people coming down with illnesses.

Still, raw food of any type is riskier. A study conducted by the FDA found that raw pet food was more likely to be contaminated with salmonella or listeria compared to non raw pet foods sampled for the study. The FDA is mostly concerned about humans. Handling raw meat at home can expose pet owners to the bacteria, and could potential make you, well, sick as a dog.

Pets may also carry the pathogens without showing signs of sickness, and can shed germs that could make their pet owners sick, according to the Centers for Disease Control and Prevention. But dogs and cats are not immune to some of these pathogens either. Pets can get sick from salmonella and E. coli, though healthy pets will rarely become sick from listeria.

In 2012, the American Veterinary Medical Association passed a resolution discouraging feeding pets raw food diets because of the risks to their owners. But Marsden said this advice is outdated. The technology to kill pathogens, including high pressure processing and slow pasteurization, has improved dramatically since then. “If it’s done right, they’re very, very safe,” he says. “The industry leaders are taking measures to control contamination. If they weren’t, they would have contamination in every lot.”

“Most companies have stringent safety and quality control programs in place to ensure their products are contaminant-free,” says Debbie Phillips-Donaldson, editor-in-chief, Petfood Industry.

Laurie Tarkan is an award-winning health journalist who writes for The New York Times, Fortune and other publications. She is the three-time recipient of the National Health Information Awards, and won the Rose Kushner Award for Writing Achievement in the Field of Breast Cancer.

“Skye was vomiting, had diarrhea and losing weight,” said the 54-year-old from Wichita, Kansas, who explained that she has fed two-year-old Skye Purina’s Beneful products for most of the dog’s life.

“Over time, she kept getting sicker and sicker and finally wouldn’t eat,” Burgardt said. “I thought she was going to die.” It was soon after taking Skye to her veterinarian and having tests that according to Burgardt, show traces of antifreeze in the dog’s system. And so Burgardt joined a lawsuit against Purina PetCare. Her dog, she says, “is alive but not well. It’s been very upsetting. I know it was all because of Beneful.”

The suit, originally filed last February by Frank Lucido of California and then amended in June, alleged Purina failed to disclose that Beneful contains dangerous substances, such as mycotoxins and industrial-grade glycols, which are found in some antifreeze products and in human food.

Nestle’s Purina blasted the lawsuit as “false” and “unsubstantiated,” and stated that the products don’t contain “industrial grade glycol.” “There are no quality issues with Beneful,” the company said.

In the original suit, Lucido claims one of his dogs died from eating Beneful while two others became seriously ill. Beneful has been on pet store shelves since 2001. Purina PetCare, which recently bought organic pet food maker Merrick Pet Care, has more than $11 billion in annual revenues. The suit seeks $5 million in damages.

According to the lawsuit, in the past four years, there have been more than 3,000 complaints online by people saying that feeding their dogs Beneful products resulted in sickness or death. The site, ConsumerAffairs.com, contains more than a 1,000 consumer reviews of Beneful, many of them claiming their dogs were made gravely ill after eating the product.

“There’s absolutely no link between Beneful and pet illness,” said Wendy Vlieks, director of corporate public relations for Nestlé Purina’s Petcare, who added that some 15 million dogs a year eat Beneful products. “We think there’s a lot of confusion and misinformation over this due to social media.”

The original lawsuit listed just Lucido and eight other dog owners whose pets were made ill or died. In June, the lawsuit was amended to include 26 additional plaintiffs. “We want the people who were hurt by feeding Beneful to their pets to receive some compensation for their loss,” said Jeffrey Cereghino, a partner at Ram, Olson, Cereghino & Kopczynski and one of the plaintiffs’ lawyers. He’s filed a motion to have the suit be a class-action case.

Purina contends the lawsuit is without merit and their products are completely safe. Last month, the company launched a national campaign to defend Beneful, which is called, “I stand behind Beneful.” “Beneful is a safe, nutritious, high-quality dog food,” the company said, adding it looks forward to proving the case in court.

Pet food recalls

Purina isn’t the only pet food maker under fire. Last Friday, Nature’s Variety announced it’s voluntarily recalling its Instinct Raw Chicken Formula for dogs with a “Best By” date of 04/27/16 due to possible Salmonella contamination. Pet owners feeding the affected product to their animals are urged to discontinue use and monitor their pet’s health.

The Federal Drug Administration regulates pet food and FDA spokesperson JuliAnn Putnam said “it must be safe and properly labeled.” But there is no requirement that pet food products have pre-market approval by the FDA, according to the agency’s website. And critics claim food labeled as safe is really not because the FDA doesn’t really do much inspection.

“A lot of so called feed can be hideous animal waste,” said Susan Thixton, a pet food consumer advocate with a group called Association for Truth in Pet Food (ATPF).

The company pled guilty to the charges in 2010 and paid $25,000 in fines while two ChemNutra officials were sentenced to three years probation along with $5,000 in fines for each. This led to the to the biggest pet food recall in history, involving names such as Hill’s Pet Nutrition, Mars Inc., Del Monte Pet Products, as well as Purina, The Iams Co. and Procter & Gamble, that manufactured pet food using the tainted ingredients. It also included retailers like Petco, Target and Costco.

By 2011, more than $12 million was paid on 20,229 claims from the United States and Canada as a result of the case.

The ingredients in Beneful dog foods: Harmful or not?

At the heart of this Purina case is what goes into the various Beneful dog foods and the levels of these elements in the food.

Beneful products contain a colorless liquid chemical called propylene glycol that is used as a preservative and to keep foods moist; the lawsuit filed in February contends this ingredient is one of the main reasons that plaintiffs’ pets became ill or died, though that ingredient was no longer listed in the amended complaint.

The amended complaint, instead of listing propylene glycol as a food ingredient, says Purina failed to disclose that Beneful contains Industrial Grade Glycols (IGG), a a more dangerous chemical. Purina flatly denied using that ingredient in products.

“We don’t have IGG’s in our products,” said Purina’s Vlieks.

As for propylene glycol, it is used in many forms of animal feed and veterinary medicine and found in human food like butter, cake mixes and sodas. But it can also be found in non-food products like antifreeze or in a solvent. And propylene glycol is used to reduce moisture in food, among other reasons.

Dr. Bruce Levitzke, director of the Veterinary Emergency and Referral Group in Brooklyn, New York said propylene glycol is generally safe for use in dog food and human foods. But it’s not good for cats, which can’t metabolize it.

“Even in small amounts, propylene glycol can cause destruction of red blood cells in cats,” explained Levitzke, who said he had no professional relationship with Purina or any other pet food maker.

The lawsuit also raises the possibility that dogs’ illness and death are due to the presence of mycotoxins in Beneful products. Toxins produced by mold, mycotoxins can contaminate grains used in pet food. The toxins can target an animal’s liver, which could lead to death.

The FDA’s Putnam said the agency has established regulatory levels of mycotoxins that are considered safe for animals, and Beneful products meet this standard.

But the ATPF said it conducted independent testing of pet foods and found Beneful Original Dog Food Dry contained very high levels of mycotoxins that were harmful to pets. The Pet Food Institute, a trade group, has countered that claim and includes links to veterinarians’ and researchers’ articles that refer to the group’s testing as “pseudo science” and “junk science.”

So is it propylene glycol, mycotoxins, IGG, or a combination that’s harming or even killing the dogs? Or is it something altogether different — and totally unconnected to the dog food?

The plaintiffs’ lawyer Cereghino claim “independent” tests of Beneful have found enough concerning evidence that some veterinarians advise owners not to feed Beneful to their dogs. But Cereghino didn’t disclose details about these independent tests.

Purina’s Vlieks said her company’s veterinarians vigorously test for mycotoxins as well as measure which amount of propylene glycol is safe for dogs. Vlieks said Beneful is made according to high-quality human food-grade levels when it comes to measuring amounts of propylene glycol.

One veterinarian contacted by Fortune agreed. “Responsible manufacturers, such as Purina, test the ingredients they receive from suppliers to ensure they are safe to use in making pet foods instead of just taking the suppliers word for it,” said Dr. Julio Lopez, a veterinarian at Studio City Animal Hospital in Los Angeles.

Lopez said he’s not being paid by Purina or any pet food company but Purina does refer media outlets to him to respond to the current lawsuit.

What about other dog food makers?

Mars Petcare wouldn’t disclose the ingredients in its products. In response to Fortune’s queries, a company spokesperson sent an email, saying, “We hold our finished products until test results confirm our quality standards are met.” The third largest pet food maker, Hill Pet Nutrition did not respond to requests for comment.

Products are required to have ingredient labels, but one study last year found that there was a high rate of mislabeling among pet food.

Kurt Gallagher, who is director of communications for the trade group the Pet Food Institute, points out that just because a dog got ill or died after eating Beneful food doesn’t mean the product caused the illness.

“Owners want answers and there’s a lot of misinformation out there,” he said. “There’s not much out there to substantiate the claims against Purina. The nation’s dog food supply is safe.”

But there’s a wrinkle of sorts to the case. The amended lawsuit filed in June charges that Purina offered cash settlements with non-disclosure agreements to some of the plaintiffs.

As for the alleged cash settlements, Vlieks said that it’s common for Purina to reach out to help customers who have complaints. She said that Purina had heard from four of the plaintiffs but no contact resulted in paid claims.

Cereghino said the case is still in the discovery phase and could that could take months. But Purina could have legal precedence on its side. A previous class action lawsuit filed in U.S district court in Missouri claimed Purina’s Beneful dog food caused severe harm and death to dogs was dismissed in January of 2014 for insufficient proof that Purina misrepresented their dog food.

Purina, meanwhile, says it is confident it will disprove this lawsuit in court. “We stand behind Beneful, which is a safe, nutritious, high quality food that millions of dogs enjoy every day,” a Purina spokesperson told Fortune. “Cases likes this cheapen the true pursuit of pet health and nutrition by stoking social media hysteria.”

But Purina is facing another legal challenge over alleged mislabeling of bacon dog treats. The class action suit contends the treats were advertised as being made mostly of real bacon, when in fact the meat is only a miniscule portion of the pet treats.

“It says on package, ‘dog’s don’t know it’s not bacon’ and we want dogs to think it is bacon, but it’s not bacon,” said Vlieks. “We’re not misleading anybody.”

Mark Koba is a freelance journalist living in New Jersey. You can follow him at @mkoba1234.

This story was corrected and revised to include more of Purina’s statements and more throughly reflect the company’s position. An earlier version didn’t sufficiently make clear that the amended lawsuit had dropped mention of propylene glycol and now mentions industrial grade glycols (IGG) as an ingredient that allegedly harmed pets. (Purina flatly denies that its products contain IGG.) The earlier version also incorrectly stated that one of the largest cases of pet poisoning was in 2008; it was in 2007.

Pet food wars: David v. Goliath edition

FORTUNE — At first glance, pet food might appear to be an enviably sedate industry. Although it was plunged into turmoil seven years ago with the discovery of contaminated ingredients, the market regrouped and has grown steadily as more people treat — and feed — dogs and cats like members of the family.

But underneath the seemingly serene surface, disputes are roiling the multi-billion dollar industry as larger, established marketers contest claims made by the upstarts. At least one newcomer is fighting back.

Purina Petcare Co., the pet-food giant founded 85 years ago, is taking on Blue Buffalo Co., which sells premium pet food, with a lawsuit filed in federal court accusing the upstart of falsely advertising its products and disparaging competitors.

Founded in 2003 by William Bishop, Blue Buffalo has backing from the private equity firm Invus Group. The Wilton, Conn.-based company had around $600 million in revenue last year, largely from sales of its Blue Basics line for pets with food allergies, its Wilderness line, which has a higher proportion of meat, and its grain-free Freedom products.

Purina, which is owned by Nestle and sells Beneful, Dog Chow, and a slew of other well-known pet products, is bristling over Blue Buffalo’s aggressive marketing tactics. The smaller company touts its use of the “finest natural ingredients” and knocks its competitors by name.

The lawsuit comes at a time when pet food brands are proliferating, with celebrities like chef Rachael Ray getting in on the game. As animals become a more central part of family life, concern for their welfare is driving demand for healthier and safer pet nourishment. This year, American consumers will spend some $23 billion to feed their pets, according to the American Pet Products Association, with more willing to spend larger sums for food with premium ingredients.

At the same time, pet ownership is rising — 68% of U.S. households have a pet, according to the association’s 2013-2014 National Pet Owners survey — up from 56% in 1988.

Pet owners got a major jolt when it emerged in 2007 that contaminated ingredients from China caused kidney failure in thousands of cats and dogs. As a result, many pet owners began paying much closer attention to food ingredients and to smaller companies that offered purer “human grade” ingredients.

“Consumers began to search out superior nutrition for their pets and avoid ingredients that might be harmful to dogs and cats,” says David Sprinkle, research director at market research firm Packaged Facts. “The pet parenting culture occurred at the same time consumers were also gravitating towards organic ingredients for themselves.”

Consumer concerns have underpinned the steady 5% growth rate the pet industry has enjoyed in recent years, with brand titans such as St. Louis-based Purina and Mars Inc. (which recently purchased Iams and Eukanuba) accounting for a sizable chunk of pet food sales, according to research firm Euromonitor International.

Even so, smaller competitors have been flourishing — even with heftier price tags on their products. Blue Buffalo’s stellar rise stems from its packaging and advertising, underscoring claims that its products are healthier because they contain no chicken or other poultry by-products. The company, which sells its food in pet specialty stores, advertises its claims in a chart that names competitors and scores their product ingredients against those of Blue Buffalo. Rival products — predictably — come up short against Blue Buffalo.

Another major pet food maker, Hill’s Pet Nutrition, Inc., which makes the popular Hill’s Science Diet, filed a complaint against Blue Buffalo with the National Advertising Division of the Council of Better Business Bureaus. The company said Blue Buffalo ads unfairly accused “big name dog food” of having “chicken by-product meal” as a first ingredient instead of real meat.

Blue Buffalo’s comparison chart, which is called the “True Blue Test,” rates rival products on five ingredients, including the inclusion of vegetables and fruits and chicken meal. The chart claims that Blue Buffalo is the only brand to fulfill all five criteria.

In mid-March, the industry group found that some of Blue Buffalo’s claims were misleading and urged the company to correct such allegations in its advertising. After an appeal, the firm made some adjustments to its marketing claims. Even so, Purina went to court, where it pulled no punches and said in its legal papers that “Blue Buffalo’s brand is built on a platform of dishonesty and deception.”

According to Purina, Blue Buffalo spent $50 million last year to unfairly disparage competing products. Purina said testing by an independent laboratory found that some of Blue Buffalo’s top sellers contain poultry meal, which most consumers view as a red flag that indicates lower-quality dog food.

Within a few days, Blue Buffalo struck back with a countersuit, accusing Purina of an “unfounded attack” on its integrity and product quality.

“I can assure you that we’ve never purchased one kernel of corn or one ounce of poultry by-product meal … two ingredients that Nestle Purina claims to have found in our food,” Bishop, the company’s founder and chairman, wrote on the company’s website.

Bishop, who did not respond to a request for comment, accused Purina — which largely sells its products in grocery and discount stores — of counting on “impulse purchases” that “are driven by pretty package designs that avoid the truth of what’s actually in the bag.

“Their Beneful brand is a great example of this type of sleight of hand, as the front of the bag features real beef, chicken or fish,” he wrote, “while the ingredient listing features corn and chicken by-product meal as the leading ingredients.”

Purina insists that its commitment to its four-legged clients is not “a marketing ploy or advertising slogan.”

It is unclear whether the spat will wind up in court, but while the two companies busily swap charges in public, Blue Buffalo is positioning itself for a major change. The company is exploring an initial public offering and earlier this year hired several top-name banks to advise it.

Barkbox raising $30 million to $40 million

Barkbox has begun approaching investors to raise a new round of funding worth $30 million to $40 million, according to sources familiar with the situation.

The New York-based company sells dog gear and treats by monthly subscription. As of last October, the company had grown by 10x over the year prior, hitting 100,000 subscribers who pay between $19 and $29 per month for the boxes. The company had also crossed the $25 million revenue run rate, meaning it was bringing in around $2 million per month. I’m told by potential investors that that subscriptions had grown significantly in the last six months.

Barkbox capitalizes on the “crazy dog person” trend, in which people are increasingly having dogs instead of babies. They’re spending as much money on them, too. A recent report from Quartz outlines the trend:

Barkbox doesn’t traffic in food, but all of the accessories, treats and toys a dog could want. In this category, startups like Wag.com and Petflow compete for share-of-wallet. The companies often draw comparisons to Pets.com, the company which became the symbol of dotcom-era excesses. But all signs point to the fact that the idea was good, the timing was bad. Shipping and logistics have advanced in the last fifteen years, making the delivery of pet food and gear by subscription a viable business plan.